[R] How to prepare a input data for Cytoscape

Hello,I want to use "Cytoscape"  to construct co-expression network for coding-lncoding (control/tretment situation).I calculated correlation by R for control and treatment and now I want to prepare input data for cytoscape,  I want molecules (genes and lncRNA) as nodes andcorrelation weighting

Re: [R] filter correlation data

uld have led you almost imediately to ?cor and friends? -- Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Tue, Jan 31, 2017 at 1

[R] filter correlation data

hello everybody,I have a very very huge table in R from calculating correlation,how can I filter it per spearman correlation and p-value before export it,I mean what is the function that I use?I want to select the pairs for value (r), , greater than 0.9 (directly correlated) and less than -0.9

Re: [R] caculate correlation

; > wrote: > > > Hi Elham, > Without knowing much about what coding.rpkm and ncoding.rkpm look > like, it is difficult to say. Have you tried to subset these matrices > as you do in the "cor" function and see what is returned? > > Jim > > On Tue, Jan 31, 20

Re: [R] caculate correlation

to say. Have you tried to subset these matrices as you do in the "cor" function and see what is returned? Jim On Tue, Jan 31, 2017 at 6:40 AM, Elham - via R-help <r-help@r-project.org> wrote: > for calculating correlation between coding and noncoding,first I transposed > da

[R] caculate correlation

for calculating correlation between coding and noncoding,first I transposed data ,(rows become columns) so row is control and columns are gene names.(so I have 2 matrix with same row and different column),I use these function for calculating correlation but all of spearman correlation are

[R] co-expression network of coding-noncoding genes

hello all, I have 9 experiments (human RNAseq data (control/treatment)),I did RNAseq analysis by CLC genomics,after normalization I calculated correlation, I have many pairs of coding and lncoding molecules that correlate according to their expression,I filtered them (> 0.9 and < -0.9).

[R] Access GSE Data Tables from GEO by GEOquery

hello all,I am following this link  http://genomicsclass.github.io/book/pages/GEOquery.html for importing data.but I have a problem in a step of (Access GSE Data Tables from GEO).in the example of tutorial there are 266 samples,but by this function                                               

[R] GEOquery

hello all,I am following this link  http://genomicsclass.github.io/book/pages/GEOquery.html for importing data.but I have a problem in a step of (Access GSE Data Tables from GEO).in the example of tutorial there are 266 samples,but by this function dim(pData(gse[[1]]))head(pData(gse[[1]])[,

Re: [R] help for

yes me too,but I do not have time to install and learn linux,I need tutorial based on windows On Saturday, December 31, 2016 3:50 AM, David Winsemius <dwinsem...@comcast.net> wrote: > On Dec 30, 2016, at 9:57 AM, Elham - via R-help <r-help@r-project.org> wrote: &g

Re: [R] help for

actually I do not work with linux. do you know same of this tutorial for windows? On Friday, December 30, 2016 10:16 PM, John McKown wrote: On Fri, Dec 30, 2016 at 12:08 PM, Sarah Goslee wrote: This isn't an R question, but a

[R] help for

hi all, I am following  http://bioinformatics.knowledgeblog.org/2011/06/20/analysing-microarray-data-in-bioconductor/  I need to download phenotypic data in the form of text file that describe chip names, and the source of the biological samples as well as probe that hybridised to them. I can

Re: [R] calculate correlations

onding columns of each. Since you do not tell us how you know which column is which it is hard to answer the question of how R will know. On 07/12/2016 11:26, Elham - via R-help wrote: > Hi All,I have 11 human RNA-seq data (control/treatment),The effect of various > drugs on various ca

[R] calculate correlations

Hi All,I have 11 human RNA-seq data (control/treatment),The effect of various drugs on various cancers,I want to calculate the genes-lncRna correlations for all tumors considered together for network,I did differential expression analysis and prepared normalized values (rpkm) of coding and

[R] memory allocation problem

hi everyone, I tried to run my code in RStudio,but I received this error message,what should I do? Error: cannot allocate vector of size 12.1 Gb In addition: Warning messages: 1: In cor(coding.rpkm[grep("23.C", coding.rpkm$name), -1], ncoding.rpkm[grep("23.C", : Reached total allocation of

[R] (no subject)

hi everyone,I tried to run my code in RStudio,but I received this error message,what should I do?Error: cannot allocate vector of size 12.1 Gb In addition: Warning messages: 1: In cor(coding.rpkm[grep("23.C", coding.rpkm$name), -1], ncoding.rpkm[grep("23.C", : Reached total allocation of

Re: [R] transpose rows and columns for large data

t", comment.char = "", stringsAsFactors = F, header = T) transpose_data <- t(data) -Dan On Tue, Nov 29, 2016 at 9:56 AM, Elham - via R-help <r-help@r-project.org> wrote: yes you have right about excel.by R,what should I do for transposing row and column?     On Tuesday,

Re: [R] transpose rows and columns for large data

yes you have right about excel.by R,what should I do for transposing row and column? On Tuesday, November 29, 2016 9:13 PM, David Winsemius <dwinsem...@comcast.net> wrote: > On Nov 29, 2016, at 9:22 AM, Elham - via R-help <r-help@r-project.org> wrote: > >

[R] transpose rows and columns for large data

Hi, I am trying to transpose large datasets inexcel (44 columns and 57774 rows) but it keeps giving me the message we can'tpaste because copy area and paste area aren't the same size. Is there a way totranspose all the data at one time instead of piece by piece? One dataset has agreat amount

[R] Duplicate row.names of lncRNA

I want to do meta analysis for lncRNA,but there is this error : Duplicate row.names are not allowed.  so 35 genes that are duplicate were detected,for example: PGM5-AS1-001 ENST0417887.1       PGM5-AS1-001 ENST0613309.4      when I search them in ensembl by its Transcript ID, one of them

[R] Duplicate row.names of lncRNA

I want to do meta analysis for lncRNA,but there is this error : Duplicate row.names are not allowedso some genes that are duplicate were detected,for example:PGM5-AS1-001 ENST0417887.1PGM5-AS1-001 ENST0613309.4when I search them in ensembl by its Transcript ID, one of them is antisense

[R] convert matrix

Dear Madam / Sir,I saw this function for "Convert to matrix as it is that you wanted" > test2<-as.matrix(test1) > colnames(test2)<-NULL > genelist<-c("Fkh2","Swi5","Sic1") > rownames(test2)<-genelist > test2 > #  [,1]  [,2]  [,3] > #Fkh2 0.141 0.242 0.342 > #Swi5 0.224 0.342 0.334 > #Sic1

[R] (no subject)

Dear Madam / Sir,I saw this function for "Convert to matrix as it is that you wanted" > test2<-as.matrix(test1) > colnames(test2)<-NULL > genelist<-c("Fkh2","Swi5","Sic1") > rownames(test2)<-genelist > test2 > #  [,1]  [,2]  [,3] > #Fkh2 0.141 0.242 0.342 > #Swi5 0.224 0.342 0.334 > #Sic1